Genome-wide high-resolution SNP-array analysis of childhood melanocytic tumor with ambiguous histopathological features

In our clinical practice, we perform genome-wide high-resolution SNP-array analysis as an adjunct to the histopathologic diagnosis for diagnostically challenging melanocytic tumors. The concept of using array-based DNA copy number analysis to screen for gene fusions associated with unbalanced genomic aberrations flanking the fusion points was applied in the diagnostic setting, and intragenic copy number changes involving common receptor kinase genes are typically further analyzed and, if necessary, studied by alternative methods. Here we present the discovery of recurrent NTRK3 gene rearrangements in childhood melanocytic neoplasms based on genome-wide high-resolution SNP-array analysis. Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from paraffin embedded formalin fixed tumor tissues from 4 childhood melanocytic tumors. Genome-wide DNA copy number alterations and allelic imbalances were analyzed.